Just to chime in on the "why" - the Hype Javascript API for goToTimeInTimelineNamed() uses the current scene. An instant transition changes the current scene instantly, but when using a different transition the current scene is still the older one (the source) until the transition has finished. Thus the goToTimeInTimelineNamed() call is not operating on the destination scene but the source scene. I do consider it a design flaw, but unlikely to be resolved anytime soon as we don't often make API changes.